EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)

BackgroundStructural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools.ResultsThe EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site http://www.immuneepitope.org through the quick link 'Browse Records by 3D Structure.'ConclusionThe EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required.

[1]  Steve Wilson,et al.  The Immune Epitope Database and Analysis Resource: From Vision to Blueprint , 2005, PLoS biology.

[2]  A. Bondi.  van der Waals Volumes and Radii , 1964 .

[3]  Jian Huang,et al.  CED: a conformational epitope database , 2006, BMC Immunology.

[4]  Alexey Bochkarev,et al.  An epidemiologically significant epitope of a 1998 human influenza virus neuraminidase forms a highly hydrated interface in the NA-antibody complex. , 2005, Journal of molecular biology.

[5]  W. Delano.  The PyMOL Molecular Graphics System (2002) , 2002 .

[6]  O. Lund,et al.  The Immune Epitope Database and Analysis Resource: From Vision to Blueprint , 2005, PLoS biology.

[7]  P E Bourne,et al.  The protein kinase resource. , 1997, Trends in biochemical sciences.

[8]  J. Thornton,et al.  Ion-pairs in proteins. , 1983, Journal of molecular biology.

[9]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[10]  Andreas Prlic,et al.  Adding Some SPICE to DAS , 2005, ECCB/JBI.

[11]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[12]  Harald Schumny,et al.  Next generation , 2005, Comput. Stand. Interfaces.

[13]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[14]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[15]  Qing Zhang,et al.  The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications , 2005, BMC Bioinformatics.

[16]  Avner Schlessinger,et al.  Epitome: database of structure-inferred antigenic epitopes , 2005, Nucleic Acids Res..